Mercurial > repos > galaxyworks > seqprep

annotate seqlens.py @ 0:f25733322c54 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 85099b149e64f24060848cb04c680e0ac8061d76"
author galaxyworks
date Fri, 26 Feb 2021 04:26:20 +0000
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Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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0
f25733322c54 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 85099b149e64f24060848cb04c680e0ac8061d76"
galaxyworks
parents:
diff changeset
1 #!/usr/bin/env python
f25733322c54 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 85099b149e64f24060848cb04c680e0ac8061d76"
galaxyworks
parents:
diff changeset
2 from collections import defaultdict
f25733322c54 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 85099b149e64f24060848cb04c680e0ac8061d76"
galaxyworks
parents:
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3 from operator import itemgetter
f25733322c54 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 85099b149e64f24060848cb04c680e0ac8061d76"
galaxyworks
parents:
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4 from sys import stdin
f25733322c54 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 85099b149e64f24060848cb04c680e0ac8061d76"
galaxyworks
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5
f25733322c54 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 85099b149e64f24060848cb04c680e0ac8061d76"
galaxyworks
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6
f25733322c54 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 85099b149e64f24060848cb04c680e0ac8061d76"
galaxyworks
parents:
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7 seqlens = defaultdict(int)
f25733322c54 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 85099b149e64f24060848cb04c680e0ac8061d76"
galaxyworks
parents:
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8 next_line_seq = False
f25733322c54 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 85099b149e64f24060848cb04c680e0ac8061d76"
galaxyworks
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9 count = 0
f25733322c54 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 85099b149e64f24060848cb04c680e0ac8061d76"
galaxyworks
parents:
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10 for line in stdin:
f25733322c54 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 85099b149e64f24060848cb04c680e0ac8061d76"
galaxyworks
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11 count += 1
f25733322c54 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 85099b149e64f24060848cb04c680e0ac8061d76"
galaxyworks
parents:
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12 if line.startswith("@"):
f25733322c54 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 85099b149e64f24060848cb04c680e0ac8061d76"
galaxyworks
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13 count = 0
f25733322c54 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 85099b149e64f24060848cb04c680e0ac8061d76"
galaxyworks
parents:
diff changeset
14 next_line_seq = True
f25733322c54 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 85099b149e64f24060848cb04c680e0ac8061d76"
galaxyworks
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15
f25733322c54 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 85099b149e64f24060848cb04c680e0ac8061d76"
galaxyworks
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16 if next_line_seq and count == 1:
f25733322c54 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 85099b149e64f24060848cb04c680e0ac8061d76"
galaxyworks
parents:
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17 next_line_seq = False
f25733322c54 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 85099b149e64f24060848cb04c680e0ac8061d76"
galaxyworks
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18 seqlens[len(line)] += 1
f25733322c54 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 85099b149e64f24060848cb04c680e0ac8061d76"
galaxyworks
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19
f25733322c54 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 85099b149e64f24060848cb04c680e0ac8061d76"
galaxyworks
parents:
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20 for (length, count) in sorted(seqlens.items(), key=itemgetter(0), reverse=True):
f25733322c54 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 85099b149e64f24060848cb04c680e0ac8061d76"
galaxyworks
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21 print("%d\t%d" % (length, count))